University of Zurich

Feb 7-8, 2019

9:30 am - 5:30 pm

Instructors:
Lachlan Deer, Julian Langer, Ulrich Bergmann

Helpers:
Stephan Schmeing, Bret Benheim

General Information

Software Carpentry
aims to help researchers get their work done
in less time and with less pain
by teaching them basic research computing skills.
This hands-on workshop will cover basic concepts and tools,
including program design, version control, data management,
and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.

Who:
The course is aimed at members of UZH: students, researchers, administrative and technical staff.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.

Requirements: Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges
on. They should have a few specific software packages installed (listed
below). They are also required to abide by
Software Carpentry's
Code of Conduct.

Accessibility: We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:

The room is wheelchair / scooter accessible.

Accessible restrooms are available.

Materials will be provided in advance of the workshop and
large-print handouts are available if needed by notifying the
organizers in advance. If we can help making learning easier for
you (e.g. sign-language interpreters, lactation facilities) please
get in touch (using contact details below) and we will
attempt to provide them.

Workshop Registration

The workshop is fully subscribed and registration is currently CLOSED.

Students and staff at the University of Zurich will recieve priority access to the workshop.
Once the workshop is filled, you will receive a non-automated email confirming your registration for the workshop.

If you are interested in registering for a waitlist or in attending future workshops please let us know by completing the following form:

The Bash Shell

Windows

Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.

Select “Use the nano editor by default” and click on “Next”.

Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.

If your "HOME" environment variable is not set (or you don't know what this is):

Open command prompt (Open Start Menu then type cmd and press [Enter])

Type the following line into the command prompt window exactly as shown:

setx HOME "%USERPROFILE%"

Press [Enter], you should see SUCCESS: Specified value was saved.

Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

macOS

The default shell in all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.

Git

Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser (current versions of Chrome, Firefox or Safari,
or Internet Explorer version 9 or above).

You will need an account at github.com
for parts of the Git lesson. Basic GitHub accounts are free. We encourage
you to create a GitHub account if you don't have one already.
Please consider what personal information you'd like to reveal. For
example, you may want to review these
instructions
for keeping your email address private provided at GitHub.

Windows

Git should be installed on your computer as part of your Bash
install (described above).

macOS

For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.

Linux

If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+Q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.

Others editors that you can use are
Notepad++ or
Sublime Text.
Be aware that you must
add its installation directory to your system path.
Please ask your instructor to help you do this.

macOS

nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.

R

Windows

Install R by downloading and running
this .exe file
from CRAN.
Also, please install the
RStudio IDE.
Note that if you have separate user and admin accounts, you should run the
installers as administrator (right-click on .exe file and select "Run as
administrator" instead of double-clicking). Otherwise problems may occur later,
for example when installing R packages.

macOS

Linux

You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo dnf install R). Also, please install the
RStudio IDE.